[2023-03-17 03:50:13,865] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:13,865] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:13,865] [INFO] DQC Reference Directory: /var/lib/cwl/stga407557d-11b6-4ecf-a5df-220471796f7a/dqc_reference
[2023-03-17 03:50:15,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:15,102] [INFO] Task started: Prodigal
[2023-03-17 03:50:15,102] [INFO] Running command: cat /var/lib/cwl/stga5ad1161-3948-4c76-a0a5-fee6cd6f7093/OceanDNA-b29825.fa | prodigal -d OceanDNA-b29825/cds.fna -a OceanDNA-b29825/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:22,439] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:22,440] [INFO] Task started: HMMsearch
[2023-03-17 03:50:22,440] [INFO] Running command: hmmsearch --tblout OceanDNA-b29825/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga407557d-11b6-4ecf-a5df-220471796f7a/dqc_reference/reference_markers.hmm OceanDNA-b29825/protein.faa > /dev/null
[2023-03-17 03:50:22,643] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:22,644] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga5ad1161-3948-4c76-a0a5-fee6cd6f7093/OceanDNA-b29825.fa]
[2023-03-17 03:50:22,656] [INFO] Query marker FASTA was written to OceanDNA-b29825/markers.fasta
[2023-03-17 03:50:22,656] [INFO] Task started: Blastn
[2023-03-17 03:50:22,656] [INFO] Running command: blastn -query OceanDNA-b29825/markers.fasta -db /var/lib/cwl/stga407557d-11b6-4ecf-a5df-220471796f7a/dqc_reference/reference_markers.fasta -out OceanDNA-b29825/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:23,222] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:23,222] [INFO] Selected 24 target genomes.
[2023-03-17 03:50:23,223] [INFO] Target genome list was writen to OceanDNA-b29825/target_genomes.txt
[2023-03-17 03:50:23,239] [INFO] Task started: fastANI
[2023-03-17 03:50:23,239] [INFO] Running command: fastANI --query /var/lib/cwl/stga5ad1161-3948-4c76-a0a5-fee6cd6f7093/OceanDNA-b29825.fa --refList OceanDNA-b29825/target_genomes.txt --output OceanDNA-b29825/fastani_result.tsv --threads 1
[2023-03-17 03:50:36,307] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:36,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga407557d-11b6-4ecf-a5df-220471796f7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:36,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga407557d-11b6-4ecf-a5df-220471796f7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:36,307] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:50:36,307] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:50:36,307] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-17 03:50:36,308] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29825/tc_result.tsv
[2023-03-17 03:50:36,308] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:36,308] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:36,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga407557d-11b6-4ecf-a5df-220471796f7a/dqc_reference/checkm_data
[2023-03-17 03:50:36,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:36,314] [INFO] Task started: CheckM
[2023-03-17 03:50:36,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29825/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29825/checkm_input OceanDNA-b29825/checkm_result
[2023-03-17 03:51:00,673] [INFO] Task succeeded: CheckM
[2023-03-17 03:51:00,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 03:51:00,675] [INFO] ===== Completeness check finished =====
[2023-03-17 03:51:00,675] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:51:00,675] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29825/markers.fasta)
[2023-03-17 03:51:00,676] [INFO] Task started: Blastn
[2023-03-17 03:51:00,676] [INFO] Running command: blastn -query OceanDNA-b29825/markers.fasta -db /var/lib/cwl/stga407557d-11b6-4ecf-a5df-220471796f7a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29825/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:51:01,596] [INFO] Task succeeded: Blastn
[2023-03-17 03:51:01,597] [INFO] Selected 21 target genomes.
[2023-03-17 03:51:01,597] [INFO] Target genome list was writen to OceanDNA-b29825/target_genomes_gtdb.txt
[2023-03-17 03:51:01,912] [INFO] Task started: fastANI
[2023-03-17 03:51:01,912] [INFO] Running command: fastANI --query /var/lib/cwl/stga5ad1161-3948-4c76-a0a5-fee6cd6f7093/OceanDNA-b29825.fa --refList OceanDNA-b29825/target_genomes_gtdb.txt --output OceanDNA-b29825/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:51:11,934] [INFO] Task succeeded: fastANI
[2023-03-17 03:51:11,936] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:51:11,937] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_017856985.1	s__Planktomarina sp017856985	93.8285	361	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	99.41	99.40	0.91	0.87	5	-
GCA_905182325.1	s__Planktomarina sp905182325	81.589	269	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698165.1	s__Planktomarina sp002698165	77.5968	114	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:51:11,937] [INFO] GTDB search result was written to OceanDNA-b29825/result_gtdb.tsv
[2023-03-17 03:51:11,937] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:51:11,937] [INFO] DFAST_QC result json was written to OceanDNA-b29825/dqc_result.json
[2023-03-17 03:51:11,938] [INFO] DFAST_QC completed!
[2023-03-17 03:51:11,938] [INFO] Total running time: 0h0m58s